Multivar_Mine Report

INDIVIDUAL SOURCE ANALYSIS (mfa)

GI_Functions (pca)

Dimensionality reduction

This section encompasses a general overview of the dimensionality reduction analysis applied.

Inertia plot: % of total variance by PC

Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.

Sample coordinates

This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.

Categorical variables

This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.

Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.

TOP active quantitative variables

This table summarizes the top 10 active quantitative variables associated with PCs.
factor dimension correlation p.value
Mobilome..prophages..transposons PC1 -0.472841643192453 6.15041240032641e-09
Intracellular.trafficing.and.secretion PC1 -0.324793805636215 0.000114374262992186
Cell.motility PC1 -0.298706895191537 0.000411905309539951
Replication.and.repair PC1 -0.237919071097978 0.00528471782631573
Extracellular.structures PC1 -0.219903765226463 0.0100997833917303
Defense.mechanisms PC1 0.23458901411206 0.00597823982479987
Secondary.structures PC1 0.485955442280858 2.0074056715733e-09
Cell.cycle.control.and.mitosis PC1 0.533501750236788 2.27273535227714e-11
Lipid.metabolism PC1 0.59109305830561 3.56950085489282e-14
Cell.wall.membrane.envelop.biogenesis PC1 0.609170162020909 3.57348670904284e-15
Defense.mechanisms PC10 -0.360511310915673 1.62274712493318e-05
Replication.and.repair PC10 -0.341676613920923 4.68051127817089e-05
General.Functional.Prediction.only PC10 -0.25842178037577 0.00238435117919244
Amino.Acid.metabolis.and.transport PC10 -0.173381440653954 0.0435278237316145
Intracellular.trafficing.and.secretion PC10 0.171511859956103 0.0458781714890851
Cell.wall.membrane.envelop.biogenesis PC10 0.224196418648199 0.00869258222788807
Coenzyme.metabolism PC10 0.356755114377824 2.01530836434371e-05
Translation PC10 0.65212335279608 8.00518864472726e-18
Translation PC11 -0.37635791554854 6.31056518324304e-06
Replication.and.repair PC11 -0.194009989592265 0.0236239441596335
Inorganic.ion.transport.and.metabolism PC11 -0.188800836493866 0.0277154285636035
Extracellular.structures PC11 0.248846437423454 0.00348533789867479
Transcription PC11 0.273663135135642 0.00126525828485413
Coenzyme.metabolism PC11 0.781661283211009 2.94844891265095e-29
Post.translational.modification..protein.turnover..chaperone.functions PC12 -0.388745821345798 2.91138269422679e-06
Secondary.structures PC12 -0.330644834305453 8.44095346315854e-05
Nucleotide.metabolism.and.transport PC12 -0.298320784571616 0.000419423859301826
Energy.production.and.conversion PC12 -0.239379231618089 0.00500397580338435
Transcription PC12 -0.186995284078657 0.0292679736943235
Function.Unknown PC12 0.184318872869083 0.0317051310220625
Cell.motility PC12 0.214221064363202 0.0122690639753596
General.Functional.Prediction.only PC12 0.219171242254594 0.0103589780968205
Translation PC12 0.369360341565254 9.63526256266088e-06
Defense.mechanisms PC12 0.391369296818932 2.46137482818066e-06
Extracellular.structures PC13 -0.345183490030987 3.86225754396452e-05
Cell.wall.membrane.envelop.biogenesis PC13 -0.311256395201959 0.000225675542085128
Transcription PC13 -0.279748099744228 0.000972396290392243
Cell.cycle.control.and.mitosis PC13 0.178995286988928 0.0370667402098804
Lipid.metabolism PC13 0.290587927433731 0.00059938389521618
Nucleotide.metabolism.and.transport PC13 0.561847283871847 1.10657766620251e-12
Mobilome..prophages..transposons PC14 -0.442559299816504 6.86463674315646e-08
Lipid.metabolism PC14 -0.228814396778808 0.00737486198265563
Signal.Transduction PC14 0.21371117324897 0.01248232917646
Nucleotide.metabolism.and.transport PC14 0.2462616864178 0.00385221182911212
Extracellular.structures PC14 0.282911608523165 0.00084601244737076
Carbohydrate.metabolism.and.transport PC14 0.346962267912726 3.50050618032942e-05
Function.Unknown PC14 0.483098216638752 2.57238002695544e-09
Carbohydrate.metabolism.and.transport PC15 -0.509882974934441 2.2947199398636e-10
Transcription PC15 -0.231453878193471 0.00670410038874723
Cell.wall.membrane.envelop.biogenesis PC15 -0.177534339393392 0.0386650845641255
General.Functional.Prediction.only PC15 0.178269058501704 0.0378541746606577
Secondary.structures PC15 0.291669279087419 0.000570535484350269
Function.Unknown PC15 0.335956367366423 6.37226938716549e-05
Inorganic.ion.transport.and.metabolism PC15 0.372215396983704 8.11686243170532e-06
Post.translational.modification..protein.turnover..chaperone.functions PC16 -0.339683140229466 5.21541929454698e-05
Intracellular.trafficing.and.secretion PC16 -0.332665083058209 7.58951517376723e-05
Transcription PC16 -0.23637873143548 0.00559604334415124
General.Functional.Prediction.only PC16 -0.213764977969403 0.0124596728636367
Function.Unknown PC16 -0.169837381372517 0.048072079113525
Secondary.structures PC16 0.196854897621906 0.0216166423204803
Carbohydrate.metabolism.and.transport PC16 0.248458042254363 0.00353837792366215
Amino.Acid.metabolis.and.transport PC16 0.342412087568313 4.49649200560299e-05
Extracellular.structures PC16 0.397702411690339 1.63133904630359e-06
Signal.Transduction PC17 -0.370103731988237 9.2159431603715e-06
Extracellular.structures PC17 -0.255346314056296 0.00269768685794672
Mobilome..prophages..transposons PC17 -0.182334320808821 0.033621501605832
Defense.mechanisms PC17 -0.17753276064907 0.0386668426163357
General.Functional.Prediction.only PC17 -0.169755512940537 0.048181540561196
Secondary.structures PC17 0.297142385433145 0.00044316085454755
Cell.motility PC17 0.301785806754949 0.000356257399749675
Transcription PC17 0.310180568657796 0.000237872841594993
Defense.mechanisms PC18 -0.215887746025238 0.0115940693659054
Cell.motility PC18 -0.206180652083758 0.0160314267734711
Intracellular.trafficing.and.secretion PC18 0.209596451180124 0.0143254045849199
Inorganic.ion.transport.and.metabolism PC18 0.296271156204298 0.000461500874240087
Cell.wall.membrane.envelop.biogenesis PC18 0.304490892894601 0.000313190340671288
Amino.Acid.metabolis.and.transport PC18 0.376902454330064 6.10360361847121e-06
Intracellular.trafficing.and.secretion PC2 -0.396415817917492 1.77473645899535e-06
Replication.and.repair PC2 -0.36576849688656 1.19278040253082e-05
Cell.wall.membrane.envelop.biogenesis PC2 -0.283470264966312 0.000825325790294407
Extracellular.structures PC2 -0.232796963447844 0.00638406448536052
Cell.motility PC2 -0.219573834041074 0.0102158104384452
General.Functional.Prediction.only PC2 0.214519192981241 0.0121458541731683
Post.translational.modification..protein.turnover..chaperone.functions PC2 0.34279791251902 4.40269122819532e-05
Carbohydrate.metabolism.and.transport PC2 0.364238442806958 1.30530527870836e-05
Inorganic.ion.transport.and.metabolism PC2 0.577957642786314 1.74089282070678e-13
Energy.production.and.conversion PC2 0.620289540555641 8.05460354637705e-16
Inorganic.ion.transport.and.metabolism PC3 -0.36662929824052 1.1335641335735e-05
Mobilome..prophages..transposons PC3 -0.317596634801948 0.000164811472380228
Defense.mechanisms PC3 -0.306386911715217 0.000285934196586157
Nucleotide.metabolism.and.transport PC3 -0.255386670347321 0.00269334517008521
Transcription PC3 -0.243131181194438 0.00434276557144672
Lipid.metabolism PC3 0.270347610638392 0.0014567854913082
Signal.Transduction PC3 0.272126175308495 0.00135098757030533
Cell.motility PC3 0.399659632364155 1.43412606229044e-06
Amino.Acid.metabolis.and.transport PC3 0.496636484601879 7.78293044650878e-10
Post.translational.modification..protein.turnover..chaperone.functions PC3 0.559869493707577 1.3791965174643e-12
Amino.Acid.metabolis.and.transport PC4 -0.346547731468923 3.58184958805597e-05
Post.translational.modification..protein.turnover..chaperone.functions PC4 -0.337853334194129 5.7563374430413e-05
Function.Unknown PC4 -0.280711343205355 0.000932194786094086
Defense.mechanisms PC4 -0.260998848609728 0.00214758024858753
Inorganic.ion.transport.and.metabolism PC4 0.243882656153895 0.00422015835598981
Lipid.metabolism PC4 0.279901957605931 0.000965870221535121
Carbohydrate.metabolism.and.transport PC4 0.281936923205451 0.00088324622080037
Transcription PC4 0.296595985918929 0.000454582627485516
Cell.motility PC4 0.355114730222684 2.21340936335297e-05
Signal.Transduction PC4 0.667602461594049 6.92540793020212e-19
Cell.cycle.control.and.mitosis PC5 -0.548929511765366 4.54402237199169e-12
Extracellular.structures PC5 -0.373873855490027 7.34178663084115e-06
Replication.and.repair PC5 -0.356313860179493 2.06688870324763e-05
Energy.production.and.conversion PC5 -0.239635930140058 0.00495602280292833
Inorganic.ion.transport.and.metabolism PC5 -0.178296222550744 0.0378244699825377
Lipid.metabolism PC5 -0.177471846049017 0.0387347269756392
Carbohydrate.metabolism.and.transport PC5 0.239324125338608 0.00501432394628675
General.Functional.Prediction.only PC5 0.318685270260427 0.000156042795930227
Mobilome..prophages..transposons PC5 0.397457347395303 1.65777465957757e-06
Secondary.structures PC5 0.505044495429553 3.60668149889232e-10
Function.Unknown PC6 -0.393041417335092 2.20989710395537e-06
Signal.Transduction PC6 -0.289045592188403 0.000642857478656458
Cell.wall.membrane.envelop.biogenesis PC6 -0.225238251304297 0.00837836624715674
Mobilome..prophages..transposons PC6 -0.215284953859039 0.0118343384239148
Secondary.structures PC6 0.213059022583021 0.0127598210371978
Translation PC6 0.233702844591917 0.00617595484141964
Intracellular.trafficing.and.secretion PC6 0.317325645636446 0.000167064361292061
Extracellular.structures PC6 0.398294288935676 1.56913428120686e-06
Nucleotide.metabolism.and.transport PC6 0.408460005035309 7.95305530288294e-07
General.Functional.Prediction.only PC6 0.541933451233532 9.5251541940114e-12
Replication.and.repair PC7 -0.429626188037926 1.79456695193907e-07
Defense.mechanisms PC7 -0.336008146736702 6.35466812498391e-05
Coenzyme.metabolism PC7 -0.310701893187542 0.000231887861465985
Lipid.metabolism PC7 0.219926972710041 0.0100916658545231
Amino.Acid.metabolis.and.transport PC7 0.233157883472388 0.00630041346368417
Extracellular.structures PC7 0.249170246349511 0.00344166591816287
Transcription PC7 0.301326347515946 0.000364094728434913
Mobilome..prophages..transposons PC7 0.318800936154662 0.000155137101904943
Cell.cycle.control.and.mitosis PC7 0.32659600081064 0.000104225546061949
Function.Unknown PC7 0.428715109675684 1.91738783184588e-07
Transcription PC8 -0.478834951603232 3.7085759901921e-09
Translation PC8 -0.328595666525044 9.39512902677123e-05
Replication.and.repair PC8 -0.300792962753531 0.000373392842488815
Cell.motility PC8 0.27356042317446 0.00127082873462408
Carbohydrate.metabolism.and.transport PC8 0.280833651625068 0.000927200592227093
Energy.production.and.conversion PC8 0.391325680842697 2.4682845362125e-06
Intracellular.trafficing.and.secretion PC8 0.546030444570452 6.18783760341068e-12
Replication.and.repair PC9 -0.426599465360426 2.23433042679363e-07
Carbohydrate.metabolism.and.transport PC9 -0.31612752383122 0.000177372566215845
General.Functional.Prediction.only PC9 -0.231895549779243 0.00659731770359058
Translation PC9 -0.178501593458086 0.0376005247265957
Transcription PC9 0.228783344912046 0.00738309517632219
Signal.Transduction PC9 0.233056897063334 0.00632372040198717
Nucleotide.metabolism.and.transport PC9 0.29424686399782 0.000506849485144157
Amino.Acid.metabolis.and.transport PC9 0.297120157725449 0.000443620279809341
Cell.motility PC9 0.410014587117973 7.15380036988163e-07
Defense.mechanisms PC9 0.444298184679724 6.01409773769871e-08

HCPC

This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 18 first relevant PCs where used.

Hierarchical clustering of individuals18 significant PCs

This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.

HCPC coordinates

This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.

Relationship between HCPC clusters and supplementary qualitative variables

Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.
None of the clusters was significanstly associated with any experimental group

Whole_Genome_Functions (pca)

Dimensionality reduction

This section encompasses a general overview of the dimensionality reduction analysis applied.

Inertia plot: % of total variance by PC

Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.

Sample coordinates

This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.

Categorical variables

This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.

Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.

TOP active quantitative variables

This table summarizes the top 10 active quantitative variables associated with PCs.
factor dimension correlation p.value
General Functional Prediction only PC1 0.501186221369938 5.14654887516868e-10
Replication and repair PC1 0.510506351176273 2.16373724519266e-10
Carbohydrate metabolism and transport PC1 0.575722624710726 2.26375221445751e-13
Amino Acid metabolis and transport PC1 0.646855154410153 1.78316947618657e-17
Cell wall/membrane/envelop biogenesis PC1 0.647372334131465 1.64948664022855e-17
Lipid metabolism PC1 0.674930593087624 2.06426702293464e-19
Post-translational modification, protein turnover, chaperone functions PC1 0.79984243941703 1.6804568052921e-31
Cell cycle control and mitosis PC1 0.841116366378416 1.39366255495156e-37
Coenzyme metabolism PC1 0.848422315419374 7.69085459451801e-39
Translation PC1 0.899906597037237 3.84467400942689e-50
Nucleotide metabolism and transport PC2 -0.653464232871294 6.51241827746532e-18
Extracellular structures PC2 -0.444402529238823 5.96640962303832e-08
Lipid metabolism PC2 -0.370923894501372 8.77334070055364e-06
Energy production and conversion PC2 -0.33454016201041 6.8717412420006e-05
Transcription PC2 0.491657709887605 1.21538453609998e-09
Carbohydrate metabolism and transport PC2 0.506254669633526 3.22313595456012e-10
Chromatin Structure and dynamics PC2 0.506558607085361 3.13317780901834e-10
General Functional Prediction only PC2 0.534693898305361 2.0127143808787e-11
Function Unknown PC2 0.641686985514998 3.85346367944169e-17
Signal Transduction PC2 0.657082875678189 3.71182941298998e-18
Replication and repair PC3 -0.372756427812468 7.85589205978847e-06
Mobilome: prophages, transposons PC3 -0.360606738274936 1.61378246809323e-05
Function Unknown PC3 0.330117049007817 8.67765594671869e-05
Cell motility PC3 0.386871172675169 3.27962270908926e-06
Energy production and conversion PC3 0.418238878165822 4.04859111422856e-07
Defense mechanisms PC3 0.461400308178594 1.57311063435458e-08
Intracellular trafficing and secretion PC3 0.466455800972864 1.04324846603619e-08
RNA processing and modification PC3 0.582418431684113 1.02452993019144e-13
Transcription PC3 0.59290325398807 2.85311033650289e-14
Inorganic ion transport and metabolism PC3 0.701379793254235 1.92777560820473e-21
Secondary structures PC4 -0.608932660327039 3.68669462088309e-15
Chromatin Structure and dynamics PC4 -0.430330212414084 1.70484690610997e-07
Lipid metabolism PC4 -0.428939482465505 1.88641573260972e-07
Transcription PC4 -0.304290140566959 0.000316212869695466
Intracellular trafficing and secretion PC4 -0.271670552998768 0.00137740093004481
Cell cycle control and mitosis PC4 0.28345089372848 0.00082603525807613
Nucleotide metabolism and transport PC4 0.296741066360656 0.000451523714232222
Mobilome: prophages, transposons PC4 0.471726859943136 6.75001710393042e-09
Cell motility PC4 0.572690947594983 3.22231065056513e-13
Replication and repair PC4 0.574469993792038 2.62045145558587e-13
RNA processing and modification PC5 -0.58420513243763 8.26640363957247e-14
Chromatin Structure and dynamics PC5 -0.386118154665951 3.43962803605068e-06
Inorganic ion transport and metabolism PC5 -0.344536929078528 4.00223061100512e-05
Intracellular trafficing and secretion PC5 -0.34205050762325 4.58609647897841e-05
Energy production and conversion PC5 0.239222465886302 0.0050334642966715
Signal Transduction PC5 0.291924750351008 0.000563909351737824
Amino Acid metabolis and transport PC5 0.314216531017548 0.000195045067880309
Transcription PC5 0.320087461036174 0.000145387749663109
Extracellular structures PC5 0.460898891593278 1.6379230008309e-08
Cytoskeleton PC5 0.570350428907963 4.22161296299884e-13
Amino Acid metabolis and transport PC6 -0.368409988359441 1.01975944054165e-05
Intracellular trafficing and secretion PC6 -0.344267385422485 4.06197785409486e-05
Post-translational modification, protein turnover, chaperone functions PC6 -0.262146732711071 0.00204914980384747
Cytoskeleton PC6 -0.245975131204578 0.00389494979015379
Signal Transduction PC6 -0.245178575651645 0.00401599715958755
Replication and repair PC6 0.220382508738935 0.00993348684641442
Cell wall/membrane/envelop biogenesis PC6 0.223647164097065 0.00886239277095965
Inorganic ion transport and metabolism PC6 0.25676704720237 0.0025485873183057
Energy production and conversion PC6 0.435596991282347 1.15728853685782e-07
Defense mechanisms PC6 0.667196974055637 7.39773974841766e-19

HCPC

This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 6 first relevant PCs where used.

Hierarchical clustering of individuals6 significant PCs

This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.

HCPC coordinates

This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.

Relationship between HCPC clusters and supplementary qualitative variables

Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.
None of the clusters was significanstly associated with any experimental group

Relative_Mobilome_Number (pca)

Dimensionality reduction

This section encompasses a general overview of the dimensionality reduction analysis applied.

Inertia plot: % of total variance by PC

Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.

Sample coordinates

This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.

Categorical variables

This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.

Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.

TOP active quantitative variables

This table summarizes the top 10 active quantitative variables associated with PCs.
factor dimension correlation p.value
Phage number PC1 0.541946739046884 9.51192719699769e-12
TP number PC1 0.724929008024099 1.90949119298997e-23
GI number PC1 0.846585780364478 1.61586457328985e-38
TP number PC2 -0.539648505944859 1.20852731545458e-11
Phage number PC2 0.800772176344021 1.27199853282682e-31

HCPC

This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 2 first relevant PCs where used.

Hierarchical clustering of individuals2 significant PCs

This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.

HCPC coordinates

This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.

Relationship between HCPC clusters and supplementary qualitative variables

Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.
None of the clusters was significanstly associated with any experimental group

INTEGRATIVE ANALYSIS

MFA analysis

Dimensionality reduction

This section encompasses a general overview of the dimensionality reduction analysis applied.

Inertia plot: % of total variance by PC

Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.

Individual PCs contribution

This plot represents the Pearson's correlation between the PCs from the individual dimensionality reduction analysis of the variable groups and the two main integrated PCs (Dim1 and Dim2). The color represent the different variable groups and the variance summarized by the integrated PC is showed between brackets.

Representation of the sample coordinates on the two first integrated PCs

This plot represents the coordinates of the samples on the two first integrated PCs (Dim1 and Dim2) as a black dot. The colored dots represent the coordinates of the samples for each active group of variables and the colored lines represent its distance from the integrated coordinates. The variance summarized by the two first integrated PCs is showed betwwen brackets.

Categorical variables

This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.

Any supplementary qualitative variable was included on this analysis.

Coordinates of categories

This plot represent the coordinates of the samples and supplementary categories on the two first Principal Components (Dim1 and Dim2). The samples are represented in blue and the categories of each supplementary group have the same color. The percentage of explained variance is given between brackets.

TOP active qualitative variables

This table summarizes the top 10 active qualitative variables associated with PCs.
None of the categories was significantly associated with any PC Any supplementary quantitative variable was included on this analysis.

TOP active quantitative variables

This table summarizes the top 10 active quantitative variables associated with PCs.
factor dimension correlation p.value
Mobilome..prophages..transposons.y PC1 -0.742396683242056 4.51831579856432e-25
GI.number PC1 -0.735705836547234 1.96324574756325e-24
Phage.number PC1 -0.607289672222125 4.57119437249579e-15
TP.number PC1 -0.547526816599285 5.27817397040337e-12
Cell.cycle.control.and.mitosis.y PC1 0.530888420420229 2.96142864935784e-11
Coenzyme.metabolism.y PC1 0.594153152137532 2.44223539965723e-14
Translation.y PC1 0.642911333796602 3.21475231291345e-17
Cell.wall.membrane.envelop.biogenesis.y PC1 0.64477835035553 2.43469166926909e-17
Lipid.metabolism.y PC1 0.659643082245437 2.48209185644314e-18
Post.translational.modification..protein.turnover..chaperone.functions.y PC1 0.684911830176911 3.74991517120055e-20
Cell.cycle.control.and.mitosis.x PC2 -0.610121688383157 3.15291217749778e-15
Inorganic.ion.transport.and.metabolism.x PC2 -0.489218103846085 1.50812286723367e-09
Defense.mechanisms.x PC2 -0.345643268770223 3.76553007677107e-05
Replication.and.repair.y PC2 0.315121289291914 0.000186483482946368
Mobilome..prophages..transposons.x PC2 0.353831776402022 2.38096586880131e-05
Phage.number PC2 0.355163633065927 2.20724753855915e-05
Cell.motility.x PC2 0.372716305673598 7.87496970568882e-06
Secondary.structures.y PC2 0.375660697842415 6.58525599817241e-06
Carbohydrate.metabolism.and.transport.y PC2 0.378819155298281 5.42505654909151e-06
General.Functional.Prediction.only.y PC2 0.461522822557494 1.55765305181879e-08

HCPC

This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 22 first relevant PCs where used.

Hierarchical clustering of individuals22 significant PCs

This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.

HCPC coordinates

This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.

Relationship between HCPC clusters and supplementary qualitative variables

Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.
None of the clusters was significanstly associated with any experimental group